From 1f63d134f5c7307222ad46eea51f8dc47f491b96 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 23 Feb 2006 16:21:09 +0000
Subject: [PATCH] Added info_type and info_text to xref.
---
modules/Bio/EnsEMBL/DBEntry.pm | 64 +++++++++++++++++++--
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 44 +++++++++-----
modules/t/dbEntries.t | 4 +-
sql/table.sql | 5 +-
4 files changed, 96 insertions(+), 21 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBEntry.pm b/modules/Bio/EnsEMBL/DBEntry.pm
index 9382690fd1..f999c465bb 100644
--- a/modules/Bio/EnsEMBL/DBEntry.pm
+++ b/modules/Bio/EnsEMBL/DBEntry.pm
@@ -85,7 +85,9 @@ sub new_fast {
-primary_id_linkable =>$primary_id_linkable,
-display_id_linkable =>$display_id_linkable,
-priority => $priority,
- -db_display_name => $db_display_name );
+ -db_display_name => $db_display_name,
+ -info_type => $info_type,
+ -info_text => $info_text);
Description: Creates a new DBEntry object
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
@@ -104,11 +106,12 @@ sub new {
my ( $adaptor, $dbID, $primary_id, $version,
$dbname, $release, $display_id, $description,
- $primary_id_linkable, $display_id_linkable, $priority, $db_display_name) =
+ $primary_id_linkable, $display_id_linkable, $priority,
+ $db_display_name, $info_type, $info_text) =
rearrange ( ['ADAPTOR','DBID','PRIMARY_ID','VERSION',
'DBNAME','RELEASE','DISPLAY_ID','DESCRIPTION',
'PRIMARY_ID_LINKABLE','DISPLAY_ID_LINKABLE','PRIORITY',
- 'DB_DISPLAY_NAME'], @args );
+ 'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT'], @args );
$self->{'adaptor'} = $adaptor;
$self->{'dbID'} = $dbID;
@@ -124,6 +127,8 @@ sub new {
if( defined $display_id_linkable) { $self->display_id_linkable($display_id_linkable) }
if( defined $priority) { $self->priority($priority) }
if( defined $db_display_name) { $self->db_display_name($db_display_name) }
+ if( defined $info_type) { $self->db_display_name($info_type) }
+ if( defined $info_text) { $self->db_display_name($info_text) }
$self->{synonyms} = [];;
return $self;
@@ -377,7 +382,7 @@ sub priority {
Arg [1] : String $db_display_name
Example : none
Db_display_name: get/set for attribute db_display_name
- Returntype : string
+ Returntype : string; has "Projected " prepended if info_type='PROJECTION'
Exceptions : none
Caller : general
@@ -387,10 +392,59 @@ sub db_display_name {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{db_display_name} = $arg;
+ }
+
+ my $name;
+ if ($self->{info_type} eq "PROJECTION") {
+ $name = "Projected " . $self->{db_display_name};
+ } else {
+ $name = $self->{db_display_name};
+ }
+
+ return $name;
+}
+
+
+=head2 info_type
+
+ Arg [1] : String $info_type
+ Example : none
+ Info_type: get/set for attribute info_type
+ Returntype : string
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub info_type {
+ my ( $self, $arg ) = @_;
+ if( defined $arg ) {
+ $self->{info_type} = $arg;
+ }
+ return $self->{info_type};
+}
+
+
+=head2 info_text
+
+ Arg [1] : String $info_text
+ Example : none
+ Info_text: get/set for attribute info_text
+ Returntype : string
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub info_text {
+ my ( $self, $arg ) = @_;
+ if( defined $arg ) {
+ $self->{info_text} = $arg;
}
- return $self->{db_display_name};
+ return $self->{info_text};
}
+
=head2 add_synonym
Arg 1 : string $synonym
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 1b6fc54fd9..3bab0c8299 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -66,7 +66,8 @@ sub fetch_by_dbID {
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
- exDB.db_name, exDB.db_display_name, exDB.release, es.synonym
+ exDB.db_name, exDB.db_display_name, exDB.release, es.synonym,
+ exDB.info_type, exDB.info_text
FROM xref, external_db exDB
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.xref_id = ?
@@ -80,7 +81,8 @@ sub fetch_by_dbID {
while ( my $arrayref = $sth->fetchrow_arrayref()){
my ( $refID, $dbprimaryId, $displayid, $version, $desc,
$primary_id_linkable, $display_id_linkable, $priority,
- $dbname, $db_display_name, $release, $synonym) = @$arrayref;
+ $dbname, $db_display_name, $release, $synonym,
+ $info_type, $info_text) = @$arrayref;
if(!$exDB) {
$exDB = Bio::EnsEMBL::DBEntry->new
@@ -94,7 +96,9 @@ sub fetch_by_dbID {
-primary_id_linkable => $primary_id_linkable,
-display_id_linkable => $display_id_linkable,
-priority => $priority,
- -db_display_name => $db_display_name);
+ -db_display_name => $db_display_name,
+ -info_type => $info_type,
+ -info_text => $info_text);
$exDB->description( $desc ) if ( $desc );
}
@@ -137,7 +141,8 @@ sub fetch_by_db_accession {
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
- exDB.db_name, exDB.db_display_name, exDB.release, es.synonym
+ exDB.db_name, exDB.db_display_name, exDB.release, es.synonym,
+ exDB.info_type, exDB.info_text
FROM xref, external_db exDB
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.dbprimary_acc = ?
@@ -168,7 +173,7 @@ sub fetch_by_db_accession {
while ( my $arrayref = $sth->fetchrow_arrayref()){
my ( $dbID, $dbprimaryId, $displayid, $version, $desc, $dbname,$db_display_name,
$primary_id_linkable, $display_id_linkable, $priority,
- $release, $synonym) = @$arrayref;
+ $release, $synonym, $info_type, $info_text) = @$arrayref;
if(!$exDB) {
$exDB = Bio::EnsEMBL::DBEntry->new
@@ -182,7 +187,9 @@ sub fetch_by_db_accession {
-primary_id_linkable => $primary_id_linkable,
-display_id_linkable => $display_id_linkable,
-priority => $priority,
- -db_display_name=>$db_display_name);
+ -db_display_name=>$db_display_name,
+ -info_type => $info_type,
+ -info_text => $info_text);
$exDB->description( $desc ) if ( $desc );
}
@@ -269,12 +276,17 @@ sub store {
display_label = ?,
version = ?,
description = ?,
- external_db_id = ?");
- $sth->bind_param(1,$exObj->primary_id,SQL_VARCHAR);
- $sth->bind_param(2,$exObj->display_id,SQL_VARCHAR);
- $sth->bind_param(3,$exObj->version,SQL_VARCHAR);
- $sth->bind_param(4,$exObj->description,SQL_VARCHAR);
- $sth->bind_param(5,$dbRef,SQL_INTEGER);
+ external_db_id = ?,
+ info_type = ?,
+ info_text = ?");
+ $sth->bind_param(1, $exObj->primary_id,SQL_VARCHAR);
+ $sth->bind_param(2, $exObj->display_id,SQL_VARCHAR);
+ $sth->bind_param(3, $exObj->version,SQL_VARCHAR);
+ $sth->bind_param(4, $exObj->description,SQL_VARCHAR);
+ $sth->bind_param(5, $dbRef,SQL_INTEGER);
+ $sth->bind_param(6, $exObj->info_type, SQL_VARCHAR);
+ $sth->bind_param(7, $exObj->info_text, SQL_VARCHAR);
+
$sth->execute();
$dbX = $sth->{'mysql_insertid'};
@@ -653,7 +665,8 @@ sub _fetch_by_object_type {
idt.query_identity, idt.target_identity, idt.hit_start,
idt.hit_end, idt.translation_start, idt.translation_end,
idt.cigar_line, idt.score, idt.evalue, idt.analysis_id,
- gx.linkage_type
+ gx.linkage_type,
+ xref.info_type, xref.info_text
FROM xref xref, external_db exDB, object_xref oxr
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
@@ -676,7 +689,8 @@ sub _fetch_by_object_type {
$dbname, $release, $exDB_status, $exDB_db_display_name, $objid,
$synonym, $queryid, $targetid, $query_start, $query_end,
$translation_start, $translation_end, $cigar_line,
- $score, $evalue, $analysis_id, $linkage_type ) = @$arrRef;
+ $score, $evalue, $analysis_id, $linkage_type,
+ $info_type, $info_text) = @$arrRef;
my %obj_hash = (
'adaptor' => $self,
@@ -726,6 +740,8 @@ sub _fetch_by_object_type {
$exDB->display_id_linkable($display_id_linkable);
$exDB->priority($priority);
$exDB->db_display_name($exDB_db_display_name);
+ $exDB->info_type($info_type);
+ $exDB->info_text($info_text);
push( @out, $exDB );
$seen{$refID} = $exDB;
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index 16a8a0eb02..8152408221 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -89,7 +89,9 @@ my $xref = Bio::EnsEMBL::DBEntry->new
-primary_id_linkable => "0",
-display_id_linkable => "1",
-priority => "5",
- -db_display_name => "Nice friendly name"
+ -db_display_name => "Nice friendly name",
+ -info_type => "PROJECTION",
+ -info_text => "from human gene ENSG0000011111"
);
diff --git a/sql/table.sql b/sql/table.sql
index e7564a3295..adb4dcdfc6 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -655,10 +655,13 @@ CREATE TABLE xref (
display_label VARCHAR(128) not null,
version VARCHAR(10) DEFAULT '' NOT NULL,
description VARCHAR(255),
+ info_type ENUM('PROJECTION', 'MISC'),
+ info_text VARCHAR(255),
PRIMARY KEY( xref_id ),
UNIQUE KEY id_index( dbprimary_acc, external_db_id ),
- KEY display_index ( display_label )
+ KEY display_index ( display_label ),
+ KEY info_type_idx ( info_type )
) COLLATE=latin1_swedish_ci;
--
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